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(-) Description

Title :  CRYSTAL STRUCTURE OF COBT COMPLEXED WITH 2,5-DIMETHYLANILINE AND NICOTINATE MONONUCLEOTIDE
 
Authors :  C. -G. Cheong, J. Escalante-Semerena, I. Rayment
Date :  06 Mar 02  (Deposition) - 07 Sep 02  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Cobt, Cobalamin Synthetic Enzyme, Phosphoribosyltransferase, 5, 6- Dimethylbenzimidazole, Nicotinate Mononucleotide, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. G. Cheong, J. C. Escalante-Semerena, I. Rayment
Capture Of A Labile Substrate By Expulsion Of Water Molecules From The Active Site Of Nicotinate Mononucleotide:5, 6-Dimethylbenzimidazole Phosphoribosyltransferase (Cobt) From Salmonella Enterica.
J. Biol. Chem. V. 277 41120 2002
PubMed-ID: 12101181  |  Reference-DOI: 10.1074/JBC.M203535200

(-) Compounds

Molecule 1 - NICOTINATE-NUCLEOTIDE--DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE
    Chains: A
    EC Number: 2.4.2.21
    Engineered: YES
    Expression System: SALMONELLA ENTERICA
    Expression System Plasmid: PT7-5
    Expression System Strain: JE2461
    Expression System Taxid: 28901
    Expression System Vector Type: PLASMID
    Gene: COBT
    Nn: DBI PRT
    Organism Scientific: SALMONELLA ENTERICA
    Organism Taxid: 28901
    Synonym: COBT

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1NCN1Ligand/IonNICOTINATE MONONUCLEOTIDE
2XYD1Ligand/Ion2,5-DIMETHYLANILINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1NCN2Ligand/IonNICOTINATE MONONUCLEOTIDE
2XYD2Ligand/Ion2,5-DIMETHYLANILINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:32 , VAL A:84 , GLN A:88 , GLU A:317 , NCN A:991BINDING SITE FOR RESIDUE XYD A 990
2AC2SOFTWAREALA A:78 , GLU A:174 , GLY A:176 , MET A:177 , ALA A:178 , ASN A:179 , THR A:180 , GLY A:202 , ALA A:203 , GLY A:264 , PHE A:265 , LEU A:266 , SER A:291 , GLU A:293 , ARG A:314 , LEU A:315 , GLY A:316 , XYD A:990 , HOH A:1005 , HOH A:1009 , HOH A:1015 , HOH A:1021 , HOH A:1041 , HOH A:1047BINDING SITE FOR RESIDUE NCN A 991

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:160 -A:256

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1L4L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L4L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1L4L)

(-) Exons   (0, 0)

(no "Exon" information available for 1L4L)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:347
 aligned with COBT_SALTY | Q05603 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:347
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       
           COBT_SALTY     3 TLHALLRDIPAPDAEAMARAQQHIDGLLKPPGSLGRLETLAVQLAGMPGLNGTPQVGEKAVLVMCADHGVWDEGVAVSPKIVTAIQAANMTRGTTGVCVLAAQAGAKVHVIDVGIDAEPIPGVVNMRVARGCGNIAVGPAMSRLQAEALLLEVSRYTCDLAQRGVTLFGVGELGMANTTPAAAMVSVFTGSDAKEVVGIGANLPPSRIDNKVDVVRRAIAINQPNPRDGIDVLSKVGGFDLVGMTGVMLGAARCGLPVLLDGFLSYSAALAACQIAPAVRPYLIPSHFSAEKGARIALAHLSMEPYLHMAMRLGEGSGAALAMPIVEAACAMFHNMGELAASNIVLP 349
               SCOP domains d1l4la_ A: Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -1l4lA01 A:4-57,A:330-349                              1l4lA02 A:58-329  [code=3.40.50.10210, no name defined]                                                                                                                                                                                                                         1l4lA01              CATH domains
               Pfam domains ----DBI_PRT-1l4lA01 A:7-346                                                                                                                                                                                                                                                                                                                             --- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh......eeeeeeeee.hhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhh..................ee................hhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhhhhh.hhhhhh......hhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh.hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l4l A   3 TLHALLRDIPAPDAEAMARTQQHIDGLLKPPGSLGRLETLAVQLAGMPGLNGTPQVGEKAVLVMCADHGVWDEGVAVSPKIVTAIQAANMTRGTTGVCVLAAQAGAKVHVIDVGIDAEPIPGVVNMRVARGCGNIAVGPAMSRLQAEALLLEVSRYTCDLAQRGVTLFGVGELGMANTTPAAAMVSVFTGSDAKEVVGIGANLPPSRIDNKVDVVRRAIAINQPNPRDGIDVLSKVGGFDLVGMTGVMLGAARCGLPVLLDGFLSYSAALAACQIAPAVRPYLIPSHFSAEKGARIALAHLSMEPYLHMAMRLGEGSGAALAMPIVEAACAMFHNMGELAASNIVLP 349
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: DBI_PRT] (24)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (COBT_SALTY | Q05603)
molecular function
    GO:0015420    cobalamin-transporting ATPase activity    Catalysis of the reaction: ATP + H2O + cob(III)alamin(out) = ADP + phosphate + cob(III)alamin(in). Cobalamin is also known as vitamin B12.
    GO:0008939    nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity    Catalysis of the reaction: 5,6-dimethylbenzimidazole + nicotinate D-ribonucleotide = alpha-ribazole 5'-phosphate + H(+) + nicotinate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0009236    cobalamin biosynthetic process    The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
    GO:0015889    cobalamin transport    The directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0009163    nucleoside biosynthetic process    The chemical reactions and pathways resulting in the formation of any one of a family of organic molecules consisting of a purine or pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
    GO:0035461    vitamin transmembrane transport    The process in which a vitamin is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. A vitamin is one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.

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  1l4l
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  COBT_SALTY | Q05603
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  2.4.2.21
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        COBT_SALTY | Q05603: 1d0s 1d0v 1jh8 1jha 1jhm 1jho 1jhp 1jhq 1jhr 1jhu 1jhv 1jhx 1jhy 1l4b 1l4e 1l4f 1l4g 1l4h 1l4k 1l4m 1l4n 1l5f 1l5k 1l5l 1l5m 1l5n 1l5o 4kqf 4kqg 4kqh 4kqi 4kqj 4kqk

(-) Related Entries Specified in the PDB File

1d0s COBT COMPLEXED WITH 5,6-DIMETHYLBENZIMIDAZOLE
1l4b
1l4e
1l4f
1l4g
1l4h
1l4k
1l4m
1l4n
1l5f
1l5k
1l5l
1l5m
1l5n
1l5o